Contacts of the helix formed by residues 168 - 183 (chain Y) in PDB entry 5G04
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 168 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Y ILE* 4.3 7.9 - - + -
166Y GLN 4.2 8.3 - - - +
167Y ARG* 1.3 74.5 - - - +
169Y PRO* 1.3 77.1 - - - +
170Y LYS* 3.3 21.4 + - - +
171Y ILE* 2.6 34.5 + - + +
172Y ASN* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 169 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X ALA* 4.2 20.2 - - + -
49X LEU* 4.6 8.3 - - + -
167Y ARG 4.7 0.7 - - - +
168Y THR* 1.3 87.2 - - - +
170Y LYS* 1.3 59.2 - - - +
172Y ASN* 3.0 6.1 + - - +
173Y MET* 2.8 27.2 + - - +
195Y VAL* 3.1 20.6 - - + +
198Y GLN* 3.2 53.2 - - + +
199Y CYS* 5.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X ALA 4.3 9.7 + - - -
47X ALA* 3.1 35.1 + - - +
48X GLY* 5.1 6.1 - - - +
49X LEU* 4.7 6.4 - - + +
137Y GLU* 6.0 4.4 - - - +
140Y TYR* 3.9 36.7 + - + +
168Y THR* 3.2 20.0 + - - +
169Y PRO* 1.3 81.4 - - - +
171Y ILE* 1.3 73.7 + - + +
173Y MET* 3.3 10.0 + - + +
174Y MET* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Y ILE* 3.8 20.2 - - + +
137Y GLU* 5.9 1.1 - - - -
140Y TYR* 3.8 30.7 - - + -
159Y LEU* 3.7 27.6 - - + +
162Y ILE* 4.4 3.4 - - + -
167Y ARG* 3.8 27.6 - - + -
168Y THR* 2.6 50.3 + - + +
170Y LYS* 1.3 91.6 - - + +
172Y ASN* 1.3 59.2 + - - +
174Y MET* 3.3 2.3 + - - +
175Y LEU* 2.8 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 172 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164Y SER 4.9 3.2 + - - -
167Y ARG* 3.0 40.1 + - - +
168Y THR 2.9 18.6 + - - -
169Y PRO* 3.5 4.6 - - - +
171Y ILE* 1.3 76.4 - - - +
173Y MET* 1.3 55.8 + - - +
175Y LEU* 3.4 7.4 + - - +
176Y ALA* 2.8 30.0 + - - +
191Y SER* 3.6 13.5 - - - +
194Y GLU* 3.7 35.7 + - + +
195Y VAL* 3.4 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 173 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X GLY 5.8 0.2 - - - +
49X LEU* 3.5 34.1 - - + -
50X HIS 5.2 1.1 - - - +
51X SER* 5.0 9.0 - - - -
52X ASN* 3.3 33.9 - - - +
140Y TYR* 5.7 3.6 - - - +
169Y PRO 2.8 19.2 + - - +
170Y LYS* 3.6 7.4 - - + +
172Y ASN* 1.3 73.2 - - - +
174Y MET* 1.3 73.4 + - + +
176Y ALA* 3.2 8.3 + - - +
177Y ASN* 3.1 46.7 + - - +
192Y TYR* 4.9 11.7 - - + -
195Y VAL* 3.4 14.1 - - + +
205Y ALA 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 174 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140Y TYR* 3.6 36.1 - - + +
143Y ALA* 3.5 34.3 - - + -
144Y GLU* 4.3 13.5 - - - -
147Y THR* 4.6 13.0 - - + +
159Y LEU* 3.9 14.8 - - + -
170Y LYS 3.1 13.1 + - - +
171Y ILE 3.9 1.3 - - - +
173Y MET* 1.3 84.1 - - + +
175Y LEU* 1.3 62.3 + - - +
177Y ASN* 3.2 15.5 + - + +
178Y LEU* 3.0 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156Y ILE* 4.7 15.9 - - + +
159Y LEU* 4.0 35.3 - - + +
160Y ASP* 5.0 1.6 - - - +
167Y ARG* 3.1 40.4 - - - +
171Y ILE 2.8 19.8 + - - +
172Y ASN* 3.4 6.7 - - - +
174Y MET* 1.3 76.9 - - - +
176Y ALA* 1.3 62.6 + - - +
178Y LEU* 3.2 4.3 + - + +
179Y TYR* 3.0 66.4 + - + +
191Y SER* 3.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172Y ASN 2.8 16.6 + - - +
173Y MET* 3.3 10.1 - - - +
175Y LEU* 1.3 72.3 - - - +
177Y ASN* 1.3 62.2 + - - +
179Y TYR* 3.2 2.0 + - - -
180Y LYS* 3.1 21.3 + - - +
188Y SER* 3.4 13.6 + - - +
191Y SER* 3.6 21.5 - - - -
192Y TYR* 3.5 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 177 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X SER* 6.0 2.4 - - - -
173Y MET* 3.1 39.2 + - - +
174Y MET* 3.2 11.5 + - + +
176Y ALA* 1.3 74.2 - - - +
178Y LEU* 1.3 64.5 + - + +
180Y LYS* 3.3 16.2 + - - +
181Y LYS* 3.1 22.3 + - - +
192Y TYR* 2.8 27.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Y THR* 4.2 23.8 - - + +
152Y ASP* 4.3 24.6 - - - +
155Y ALA* 3.6 30.1 - - + -
156Y ILE* 4.1 22.1 - - + +
159Y LEU* 4.2 19.3 - - + -
174Y MET* 3.0 27.1 + - + +
175Y LEU* 3.2 6.9 + - - +
177Y ASN* 1.3 76.6 - - + +
179Y TYR* 1.4 61.0 + - - +
181Y LYS* 3.4 7.6 + - + +
182Y ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156Y ILE* 4.0 30.5 - - + +
160Y ASP* 4.3 17.3 + - - +
175Y LEU* 3.0 56.5 + - + +
176Y ALA* 3.7 2.7 - - - +
178Y LEU* 1.4 77.5 - - - +
180Y LYS* 1.3 48.3 + - - +
182Y ALA* 3.1 3.9 + - - +
183Y GLY 2.8 29.1 + - - -
184Y GLN* 3.0 35.7 + - + +
187Y PRO* 3.6 42.2 - - + -
188Y SER* 3.2 17.7 - - - +
191Y SER* 4.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 180 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176Y ALA 3.1 8.5 + - - +
177Y ASN* 3.5 17.5 + - - +
178Y LEU 3.3 0.4 - - - -
179Y TYR* 1.3 70.8 - - - +
181Y LYS* 1.3 67.1 + - - +
183Y GLY* 3.0 15.7 + - - +
184Y GLN 5.1 0.7 - - - +
185Y GLU* 6.3 0.2 - - - +
188Y SER* 3.0 25.3 + - - +
192Y TYR* 3.2 32.7 + - + +
204Y ASP 5.6 0.2 + - - -
208Y GLY* 4.0 14.3 - - - -
211Y SER* 4.3 12.5 + - - +
212Y LEU* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152Y ASP* 3.5 23.0 + - - +
177Y ASN 3.1 12.5 + - - +
178Y LEU* 3.7 10.1 - - + +
180Y LYS* 1.3 77.4 - - - +
182Y ALA* 1.3 63.0 + - - +
183Y GLY* 3.3 1.0 + - - -
370Y SER* 5.5 4.8 + - - -
371Y ASN* 6.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152Y ASP* 5.3 2.2 + - + -
156Y ILE* 4.5 12.6 - - + -
178Y LEU 2.9 14.8 + - - +
179Y TYR* 3.1 13.7 + - - +
181Y LYS* 1.3 78.2 - - - +
183Y GLY* 1.3 56.9 + - - +
184Y GLN* 3.5 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 183 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Y TYR 2.8 6.7 + - - -
180Y LYS* 3.0 15.3 + - - -
181Y LYS 3.2 0.9 - - - -
182Y ALA* 1.3 74.7 - - - +
184Y GLN* 1.3 61.4 + - - +
185Y GLU* 3.6 13.1 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il